Proteomics Approaches to Unravel Virus - Vertebrate Host Interactions, Volume 109 in the Advances in Virus Research series, highlights state-of-the art mass spectrometry techniques to elucidate the tight interplay of vertebrate viruses and their host cells. The volume includes chapters on Spatio-temporal resolution of host protein complexes during virus entry, Proteomic approaches to investigate gammaherpesvirus biology and associated tumorigenesis, Applications of Mass Spectrometry Imaging in Virus Research, Mapping surfaceome dynamics during viral infection, Characterization of proteolytic events in virus-host interactions, Dynamic protein network modulation upon viral infection, and much more. - Discusses the latest methodological breakthroughs in mass spectrometry-based proteomics - Reviews how technology has advanced our knowledge on virus-host interactions - Provides future perspectives on proteomics research in virology
Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases
Genetics and Evolution of Infectious Diseases, Third Edition discusses the evolving field of infectious diseases and their continued impact on the health of populations, especially in resource-limited areas of the world where they must confront the dual burden of death and disability due to infectious and chronic illnesses. Although substantial gains have been made in public health interventions for the treatment, prevention, and control of infectious diseases, in recent decades the world has witnessed the emergence of the human immunodeficiency virus (HIV) and the COVID-19 pandemic, increasing antimicrobial resistance, and the emergence of many new bacterial, fungal, parasitic, and viral pathogens. Fully updated and revised, this new edition presents the consequences of such diseases, the evolution of infectious diseases, the genetics of host-pathogen relationship, and the control and prevention strategies that are, or can be, developed. This book offers valuable information to biomedical researchers, clinicians, public health practitioners, decisions-makers, and students and postgraduates studying infectious diseases, microbiology, medicine, and public health that is relevant to the control and prevention of neglected and emerging worldwide diseases. - Takes an integrated approach to infectious diseases - Provides the latest developments in the field of infectious diseases - Focuses on the contribution of evolutionary and genomic studies for the study and control of transmissible diseases - Includes updated and revised contributions from leading authorities, along with six new chapters
Proteins are indispensable players in virtually all biological events. The functions of proteins are coordinated through intricate regulatory networks of transient protein-protein interactions (PPIs). To predict and/or study PPIs, a wide variety of techniques have been developed over the last several decades. Many in vitro and in vivo assays have been implemented to explore the mechanism of these ubiquitous interactions. However, despite significant advances in these experimental approaches, many limitations exist such as false-positives/false-negatives, difficulty in obtaining crystal structures of proteins, challenges in the detection of transient PPI, among others. To overcome these limitations, many computational approaches have been developed which are becoming increasingly widely used to facilitate the investigation of PPIs. This book has gathered an ensemble of experts in the field, in 22 chapters, which have been broadly categorized into Computational Approaches, Experimental Approaches, and Others.
New viral diseases are emerging continuously. Viruses adapt to new environments at astounding rates. Genetic variability of viruses jeopardizes vaccine efficacy. For many viruses mutants resistant to antiviral agents or host immune responses arise readily, for example, with HIV and influenza. These variations are all of utmost importance for human and animal health as they have prevented us from controlling these epidemic pathogens. This book focuses on the mechanisms that viruses use to evolve, survive and cause disease in their hosts. Covering human, animal, plant and bacterial viruses, it provides both the basic foundations for the evolutionary dynamics of viruses and specific examples of emerging diseases. - NEW - methods to establish relationships among viruses and the mechanisms that affect virus evolution - UNIQUE - combines theoretical concepts in evolution with detailed analyses of the evolution of important virus groups - SPECIFIC - Bacterial, plant, animal and human viruses are compared regarding their interation with their hosts
The field of virology has seen explosive growth in the past few decades. A large amount of effort has gone into successfully delineating virus evolution, genetic diversity, immunology, pathogenesis, structure, vaccine development, viral gene expression and genomic replication strategies. In addition, considerable recent work has been focusing on cellular responses to infection as well as how viruses may induce transformation and oncogenesis. Viruses are obligate intracellular parasites and thus absolutely dependent upon host cells. Not surprisingly, they often cause profound changes in cells, including apoptosis, death and signalling, to name a few perturbations. Thus, the molecular signals for how viruses induce pathophysiological alterations in their hosts have been of growing recent interest. Cellular and organismal responses, such as those induced by virus infection, are invariably mediated by changes in gene and protein expression and modification. Thus, there has been keen interest in understanding how gene and protein expressions and modifications are quantitatively and qualitatively affected by such challenges. From a historical perspective, most early work that examined host protein responses to virus infection employed “biased” approaches, in which investigators targeted a limited number, or only one cellular molecule of interest. Completion of many organisms’ genome sequences has allowed the global “non-biased” simultaneous analysis of the entire repertoire of cellular mRNA species, the transcriptome, by gene micro-arrays. This has provided significant information about how cellular gene expressions are altered by virus-induced perturbations, but has not provided as much information about the encoded proteins. This results for several reasons, including, but not limited to the fact that gene expression levels cannot accurately predict protein expression levels, nor the types and extent of post-translational modifications, many genes encode multiple proteins through splice variants, and protein activity may be affected by a large number of conditions, including phosphorylation. Recent technological and bioinformatic approaches make it now possible to begin to extend similar global analyses to probe the cellular proteome, the repertoire of the actual effector molecules. One general strategy has been to take advantage of improved separations technologies, as well as greatly improved mass spectrometry resolution, to quantitatively or comparatively measure hundreds or thousands of proteins. Proteins from multiple conditions (i.e., mock-infected and infected) may be differentially labelled by various techniques, such as 2D-DIGE, ICAT, iTRAQ, SILAC, with 18O during peptide preparation, and/or by various other methods, and then compared to measure comparative alterations in the levels of proteins induced by the virus infection. Such analyses have also been extended by using “label-free” methods for more efficient multiplexing applications, and/or by examining specific protein modifications. In addition, concerted efforts to raise antibodies against all cellular proteins have resulted in the development of “antibody arrays,” which are also generally used for quantitative or comparative assays. Finally, while assays, such as the above, are generally limited to delineating the absolute amount of specific proteins, newer technologies have been developed that allow the simultaneous probing of hundreds of proteins’ functions. Assays, such as “Activity Based Protein Profiling”, are designed to probe enzymatic activity, with current focus on broad-spectrum proteases and other enzymatic classes. This Research Topic will provide an overview of many of these methods, as well as numerous specific examples of each approach, and how they are used to better delineate the ways viruses affect cellular responses during infection.
This detailed volume explores state-of-the-art methods for the identification, quantification, and characterization of microbial proteins. Split into five parts, the content addresses global sample preparation and protein enrichment, subcellular fractionation, protein quantification, analysis of post-translational protein modifications, as well as metaproteomics, a relatively new branch of microbial proteomics that investigates the proteins of all microbes comprising an environmental consortium. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Microbial Proteomics: Methods and Protocols serves as a valuable and stimulating source for all beginners and advanced researchers in the field of microbial proteomics and beyond. Chapter 18 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Protocols used in Molecular Biology is a compilation of several examples of molecular biology protocols. Each example is presented with a concise introduction, materials and chemicals required, a step-by-step procedure and troubleshooting tips. Information about the application of the protocol is also provided. The techniques included in this book are essential to research in the fields of proteomics, genomics, cell culture, epigenetic modification and structural biology. The protocols can also be used by clinical researchers (neuroscientists and oncologists, for example) for medical applications (diagnostics, therapeutics and multidisciplinary projects).
Angiogenesis, the development of new blood vessels from the existing vasculature, is essential for physiological growth and over 18,000 research articles have been published describing the role of angiogenesis in over 70 different diseases, including cancer, diabetic retinopathy, rheumatoid arthritis and psoriasis. One of the most important technical challenges in such studies has been finding suitable methods for assessing the effects of regulators of eh angiogenic response. While increasing numbers of angiogenesis assays are being described both in vitro and in vivo, it is often still necessary to use a combination of assays to identify the cellular and molecular events in angiogenesis and the full range of effects of a given test protein. Although the endothelial cell - its migration, proliferation, differentiation and structural rearrangement - is central to the angiogenic process, it is not the only cell type involved. the supporting cells, the extracellular matrix and the circulating blood with its cellular and humoral components also contribute. In this book, experts in the use of a diverse range of assays outline key components of these and give a critical appraisal of their strengths and weaknesses. Examples include assays for the proliferation, migration and differentiation of endothelial cells in vitro, vessel outgrowth from organ cultures, assessment of endothelial and mural cell interactions, and such in vivo assays as the chick chorioallantoic membrane, zebrafish, corneal, chamber and tumour angiogenesis models. These are followed by a critical analysis of the biological end-points currently being used in clinical trials to assess the clinical efficacy of anti-angiogenic drugs, which leads into a discussion of the direction future studies should take. This valuable book is of interest to research scientists currently working on angiogenesis in both the academic community and in the biotechnology and pharmaceutical industries. Relevant disciplines include cell and molecular biology, oncology, cardiovascular research, biotechnology, pharmacology, pathology and physiology.
Proteomic Profiling and Analytical Chemistry: The Crossroads, Second Edition helps scientists without a strong background in analytical chemistry to understand principles of the multistep proteomic experiment necessary for its successful completion. It also helps researchers who do have an analytical chemistry background to break into the proteomics field. Highlighting points of junction between proteomics and analytical chemistry, this resource links experimental design with analytical measurements, data analysis, and quality control. This targeted point of view will help both biologists and chemists to better understand all components of a complex proteomic study. The book provides detailed coverage of experimental aspects such as sample preparation, protein extraction and precipitation, gel electrophoresis, microarrays, dynamics of fluorescent dyes, and more. The key feature of this book is a direct link between multistep proteomic strategy and quality control routinely applied in analytical chemistry. This second edition features a new chapter on SWATH-MS, substantial updates to all chapters, including proteomic database search and analytical quantification, expanded discussion of post-hoc statistical tests, and additional content on validation in proteomics. - Covers the analytical consequences of protein and peptide modifications that may have a profound effect on how and what researchers actually measure - Includes practical examples illustrating the importance of problems in quantitation and validation of biomarkers - Helps in designing and executing proteomic experiments with sound analytics
